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ParallelStructure log file (check_x86_64_linux)

Fri May 11 11:15:11 2018: Checking package ParallelStructure (SVN revision 19) ...
* using log directory ‘/srv/rf/building/build_2018-05-11-12-13/RF_PKG_CHECK/PKGS/ParallelStructure.Rcheck’
* using R version 3.5.0 Patched (2018-05-03 r74693)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ParallelStructure/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ParallelStructure’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘francois besnier ’

New submission

Non-FOSS package license (GPL3)

No package encoding and non-ASCII characters in the following R files:
  R/MPI_structure.R
    511: 					## pop_id should be 1 2..n; and n <89> K 
    523: 						message='Error : if usepopinfo is ==1 the column of prior population id should be 1..n ; and n <89> K. e.g., 
  R/parallel_structure.R
    411: 					## pop_id should be 1 2..n; and n <89> K 
    423: 						message='Error : if usepopinfo is ==1 the column of prior population id should be 1..n ; and n <89> K. e.g., 

The Title field should be in title case, current version then in title case:
‘function to run parallel jobs in STRUCTURE’
‘Function to Run Parallel Jobs in STRUCTURE’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ParallelStructure’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  GPL3
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... WARNING
Found the following files with non-ASCII characters:
  MPI_structure.R
  parallel_structure.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘Rmpi’ ‘parallel’
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls without 'PACKAGE' argument:
  .Call("mpi_finalize", ...)
  .Call("mpi_finalize", ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [5s/5s] NOTE
convert_IDs: warning in write(t(sdat), ncolumn = length(sdat[1, ]),
  file = res_name, append = T): partial argument match of 'ncolumn' to
  'ncolumns'
MPI_structure: no visible binding for global variable ‘Mac_path’
MPI_structure: no visible global function definition for ‘read.table’
MPI_structure: no visible global function definition for
  ‘mpi.spawn.Rslaves’
MPI_structure : .Last: no visible global function definition for
  ‘mpi.comm.size’
MPI_structure : .Last: no visible global function definition for
  ‘mpi.close.Rslaves’
MPI_structure : slave_fun_unix: no visible global function definition
  for ‘mpi.send.Robj’
MPI_structure : slave_fun_unix: no visible global function definition
  for ‘mpi.recv.Robj’
MPI_structure : slave_fun_unix: no visible global function definition
  for ‘mpi.any.source’
MPI_structure : slave_fun_unix: no visible global function definition
  for ‘mpi.any.tag’
MPI_structure : slave_fun_unix: no visible global function definition
  for ‘mpi.get.sourcetag’
MPI_structure : slave_fun_windows: no visible global function
  definition for ‘mpi.send.Robj’
MPI_structure : slave_fun_windows: no visible global function
  definition for ‘mpi.recv.Robj’
MPI_structure : slave_fun_windows: no visible global function
  definition for ‘mpi.any.source’
MPI_structure : slave_fun_windows: no visible global function
  definition for ‘mpi.any.tag’
MPI_structure : slave_fun_windows: no visible global function
  definition for ‘mpi.get.sourcetag’
MPI_structure: no visible global function definition for
  ‘mpi.comm.size’
MPI_structure: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
MPI_structure: no visible global function definition for
  ‘mpi.bcast.cmd’
MPI_structure: no visible global function definition for
  ‘mpi.recv.Robj’
MPI_structure: no visible global function definition for
  ‘mpi.any.source’
MPI_structure: no visible global function definition for ‘mpi.any.tag’
MPI_structure: no visible global function definition for
  ‘mpi.get.sourcetag’
MPI_structure: no visible global function definition for
  ‘mpi.send.Robj’
MPI_structure: no visible global function definition for
  ‘mpi.close.Rslaves’
MPI_structure: no visible global function definition for ‘write.csv’
convert_IDs: no visible global function definition for ‘read.table’
parallel_structure: no visible binding for global variable ‘Mac_path’
parallel_structure: no visible global function definition for
  ‘read.table’
parallel_structure: no visible global function definition for
  ‘mclapply’
parallel_structure: no visible global function definition for
  ‘write.csv’
plot_str: no visible global function definition for ‘read.table’
plot_str: no visible global function definition for ‘pdf’
plot_str: no visible global function definition for ‘barplot’
plot_str: no visible global function definition for ‘colors’
plot_str: no visible global function definition for ‘abline’
plot_str: no visible global function definition for ‘mtext’
plot_str: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  Mac_path abline barplot colors dev.off mclapply mpi.any.source
  mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd mpi.close.Rslaves
  mpi.comm.size mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
  mpi.spawn.Rslaves mtext pdf read.table write.csv
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "mtext")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'plot_str':
  ‘convert_output_ID.Rd’ ‘plot_str.Rd’
Rd files with duplicated alias 'plot_str':
  ‘convert_output_ID.Rd’ ‘plot_str.Rd’
* checking Rd line widths ... NOTE
Rd file 'MPI_structure.Rd':
  \usage lines wider than 90 characters:
     MPI_structure(joblist = NULL, n_cpu = NULL, structure_path = Mac_path, infile = NULL, outpath = NULL,get_log=1,
      numinds = NULL, numloci = NULL, plot_output = 1, label = 1, popdata = 1, popflag = 0, locdata = 0, 
      phenotypes = 0, markernames = 0, mapdist = 0, onerowperind = 0, phaseinfo = 0, recessivealleles = 0, 
      phased = 0, extracol = 0, missing = -9, ploidy = 2, noadmix = 0, linkage = 0, usepopinfo = 0, locprior = 0,
       inferalpha = 1, alpha = 1, popalphas = 0, unifprioralpha = 1, alphamax = 10, alphapropsd = 0.025, freqscorr = 1, 
       onefst = 0, fpriormean = 0.01, fpriorsd = 0.05, inferlambda = 0, lambda = 1, computeprob = 1, 
       pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0, metrofreq = 10, updatefreq = 1, printqhat = 0,revert_convert=0,
  \examples lines wider than 100 characters:
     #       MPI_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',numinds ... [TRUNCATED]
     #       MPI_structure(structure_path=Mac_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',num ... [TRUNCATED]
     #       MPI_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',numinds ... [TRUNCATED]
     #       MPI_structure(structure_path=Windows_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/' ... [TRUNCATED]

Rd file 'parallel_structure.Rd':
  \usage lines wider than 90 characters:
     MPI_structure(joblist = NULL, n_cpu = NULL, structure_path = Mac_path, infile = NULL, outpath = NULL,
      numinds = NULL, numloci = NULL, plot_output = 1, label = 1, popdata = 1, popflag = 0, locdata = 0, 
      phenotypes = 0, markernames = 0, mapdist = 0, onerowperind = 0, phaseinfo = 0, recessivealleles = 0, 
      phased = 0, extracol = 0, missing = -9, ploidy = 2, noadmix = 0, linkage = 0, usepopinfo = 0, locprior = 0,
       inferalpha = 1, alpha = 1, popalphas = 0, unifprioralpha = 1, alphamax = 10, alphapropsd = 0.025, freqscorr = 1, 
       onefst = 0, fpriormean = 0.01, fpriorsd = 0.05, inferlambda = 0, lambda = 1, computeprob = 1, 
       pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0, metrofreq = 10, updatefreq = 1, printqhat = 0,revert_convert=0,
  \examples lines wider than 100 characters:
     #       parallel_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',nu ... [TRUNCATED]
     #       parallel_structure(structure_path=Mac_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/ ... [TRUNCATED]
     #       parallel_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',nu ... [TRUNCATED]
     #       parallel_structure(structure_path=Windows_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_resu ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘convert_IDs’
Undocumented data sets:
  ‘Mac_path’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'MPI_structure':
MPI_structure
  Code: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, get_log = 1, plot_output = 1,
                 label = 1, popdata = 1, popflag = 0, locdata = 0,
                 phenotypes = 0, markernames = 0, mapdist = 0,
                 onerowperind = 0, phaseinfo = 0, recessivealleles = 0,
                 phased = 0, extracol = 0, missing = -9, ploidy = 2,
                 noadmix = 0, linkage = 0, usepopinfo = 0, locprior =
                 0, inferalpha = 1, alpha = 1, popalphas = 0,
                 unifprioralpha = 1, alphamax = 10, alphapropsd =
                 0.025, freqscorr = 1, onefst = 0, fpriormean = 0.01,
                 fpriorsd = 0.05, inferlambda = 0, lambda = 1,
                 computeprob = 1, pfromflagonly = 0, ancestdist = 0,
                 startatpopinfo = 0, metrofreq = 10, updatefreq = 1,
                 printqhat = 0, revert_convert = 0, randomize = 1, seed
                 = 1234, log10Rstart = NULL, log10Rmin = NULL,
                 log10Rmax = NULL, log10Rpropsd = NULL)
  Docs: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, get_log = 1,
                 numinds = NULL, numloci = NULL, plot_output = 1, label
                 = 1, popdata = 1, popflag = 0, locdata = 0, phenotypes
                 = 0, markernames = 0, mapdist = 0, onerowperind = 0,
                 phaseinfo = 0, recessivealleles = 0, phased = 0,
                 extracol = 0, missing = -9, ploidy = 2, noadmix = 0,
                 linkage = 0, usepopinfo = 0, locprior = 0, inferalpha
                 = 1, alpha = 1, popalphas = 0, unifprioralpha = 1,
                 alphamax = 10, alphapropsd = 0.025, freqscorr = 1,
                 onefst = 0, fpriormean = 0.01, fpriorsd = 0.05,
                 inferlambda = 0, lambda = 1, computeprob = 1,
                 pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0,
                 metrofreq = 10, updatefreq = 1, printqhat = 0,
                 revert_convert = 0, randomize = 1)
  Argument names in code not in docs:
    seed log10Rstart log10Rmin log10Rmax log10Rpropsd
  Mismatches in argument names:
    Position: 6 Code: numinds Docs: get_log
    Position: 7 Code: numloci Docs: numinds
    Position: 8 Code: get_log Docs: numloci

Codoc mismatches from documentation object 'plot_str':
convert_IDs
  Code: function(ID1 = NULL, out_nam = NULL, rev_convert = NULL,
                 printqhat = NULL, k = NULL)
  Docs: function()
  Argument names in code not in docs:
    ID1 out_nam rev_convert printqhat k

Codoc mismatches from documentation object 'parallel_structure':
MPI_structure
  Code: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, get_log = 1, plot_output = 1,
                 label = 1, popdata = 1, popflag = 0, locdata = 0,
                 phenotypes = 0, markernames = 0, mapdist = 0,
                 onerowperind = 0, phaseinfo = 0, recessivealleles = 0,
                 phased = 0, extracol = 0, missing = -9, ploidy = 2,
                 noadmix = 0, linkage = 0, usepopinfo = 0, locprior =
                 0, inferalpha = 1, alpha = 1, popalphas = 0,
                 unifprioralpha = 1, alphamax = 10, alphapropsd =
                 0.025, freqscorr = 1, onefst = 0, fpriormean = 0.01,
                 fpriorsd = 0.05, inferlambda = 0, lambda = 1,
                 computeprob = 1, pfromflagonly = 0, ancestdist = 0,
                 startatpopinfo = 0, metrofreq = 10, updatefreq = 1,
                 printqhat = 0, revert_convert = 0, randomize = 1, seed
                 = 1234, log10Rstart = NULL, log10Rmin = NULL,
                 log10Rmax = NULL, log10Rpropsd = NULL)
  Docs: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, plot_output = 1, label = 1,
                 popdata = 1, popflag = 0, locdata = 0, phenotypes = 0,
                 markernames = 0, mapdist = 0, onerowperind = 0,
                 phaseinfo = 0, recessivealleles = 0, phased = 0,
                 extracol = 0, missing = -9, ploidy = 2, noadmix = 0,
                 linkage = 0, usepopinfo = 0, locprior = 0, inferalpha
                 = 1, alpha = 1, popalphas = 0, unifprioralpha = 1,
                 alphamax = 10, alphapropsd = 0.025, freqscorr = 1,
                 onefst = 0, fpriormean = 0.01, fpriorsd = 0.05,
                 inferlambda = 0, lambda = 1, computeprob = 1,
                 pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0,
                 metrofreq = 10, updatefreq = 1, printqhat = 0,
                 revert_convert = 0, randomize = 1)
  Argument names in code not in docs:
    get_log seed log10Rstart log10Rmin log10Rmax log10Rpropsd
  Mismatches in argument names (first 3):
    Position: 8 Code: get_log Docs: plot_output
    Position: 9 Code: plot_output Docs: label
    Position: 10 Code: label Docs: popdata

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plot_str':
  ‘...’

Undocumented arguments in documentation object 'edit_params'
  ‘LocPar’ ‘GlobPar’

Objects in \usage without \alias in documentation object 'parallel_structure':
  ‘MPI_structure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

Status: 8 WARNINGs, 3 NOTEs
See
  ‘/srv/rf/building/build_2018-05-11-12-13/RF_PKG_CHECK/PKGS/ParallelStructure.Rcheck/00check.log’
for details.


Run time: 25.23 seconds.